The importance of the intestinal microflora and, more specifically its composition, in physiological and pathophysiological processes in the human GIT is becoming more evident. Examples of such processes are translocation, the production and resorption of endotoxins, immune-modulation, and colonic motility. This leads to new possibilities for prevention and therapy of diseases, mainly of the gastrointestinal organs. New discoveries are specifically related to the beneficial effects of lactobacilli which have been discussed for decades. It is possible to increase the proportion of lactobacilli in the gastrointestinal microflora by consumption of fermented dairy products or by oral administration of specific non-digestible substrates such as oligofructose. Results from clinical trials and scientific studies have confirmed the preventive and therapeutic effects of selected strains of lactobacilli in viral- and bacterial-induced intestinal infections, in positively influencing immunological parameters, in normalizing the intestinal motility, and in inhibiting metabolic events in the gut lumen which promote colonic carcinogenesis. Nevertheless, there are still unresolved issues which can only be answered by well designed and well controlled clinical trials.